Phosphorus (P) is an irreplaceable and essential nutrient for all living beings and a critical element for food production. However P is not only an essential and irreplaceable non-renewable resource, but also a potential water pollutant which can cause eutrophication. Phosphorus used in fertilizer for food, accounts for approximately 90% of the total phosphorus consumption. China's rapid urbanization calls for a better and comprehensive understanding of P management in urban food systems. In this paper, we firstly present a concept model to map the P metabolism of food production and consumption system. And then we analyzed the change of urban food P metabolism and estimated food P footprint from the year 1985 to 2010 based on the method of substance flow analysis and our definition of P footprint, taking Longyan as an example. The result demonstrated that both input P and output P increased significantly (the input P increased from 4110 t to 12102 t, the output P from 3855 t to 11315 t); the total P footprint grew up from 6482 t to 20473 t and the proportion of the direct P footprint decreased from 53% to 42%; the growth of the indirect P footprint was faster than that of the direct P footprint. The P metabolism analysis reflected that Longyan was an important P sink at the city scale and main P source at the watershed scale. Our results of P footprint analysis indicated that the indirect P footprint constituted an important proportion of the total P footprint and should not be neglected. The analysis of P footprint helped to comprehensively understand and evaluate characters of urban P metabolism. Combining the analysis of P footprint and substance flow had guiding significance for national and regional P management and regulation.